Unfortunately, I can't help much with refresh_on_change either, we just use the <conditional>/<when> tag set. I have been under the impression the the documentation has been written for 'refresh_on_change' in the meantime. I am sorry, I should have checked first, before suggesting it.
No problem. I’ll know to keep en eye for documentation on this feature :)
refresh_on_change is not a feature that is exposed to tool developers for use in tool wrappers. Instead, it's used behind the scenes to make conditional/when and dynamic options tags work.
Hmmm, ok. That explains why there are so few uses of it. May I suggest amending <http://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Cpage.3E_tag_set> to make it clearer that tool developers are not meant to use it?
Regarding the command line: you can have different commandlines, eg
<command> #if ($summary.mode=="a")#commandline1 #elif ($summary.mode=="b")#commandline2 #elif ($summary.mode=="c")#commandline3 #end if </command>
and one of those 'commandlines' could be two commands (ie indexing first, followed by the next binary)
I had not thought of that! That makes sense, yes. I’ll do that.
Frequently, if/else is used to progressively build a command line:
-- my_script.py
#if option1: --enable-option1 --option1-parameter $option1-parameter #elif option2: --enable-option1 --option1-parameter $option1-parameter #endif
Sure. I meant I had not thought of executing *several* commands in the <command> tag. Thanks, Jean-Frédéric